7NA5: PDB entry 7NA5

Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen. Determined by X-ray diffraction at 2.5 Å resolution. Released 22 Jun 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 6,689
Mol. weight: 98.38 kDa
Released: 22 Jun 2022

Explore 7NA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NA5 contains 27 α-helices and 73 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-180	16
β-strand	183	1	2
β-strand	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-224	3	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4
α-helix	276	1
α-helix	278	1

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
α-helix	90	1
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	32-38	7	9
β-strand	45-50	6	9
β-strand	54-58	5	8
β-strand	61-66	6	8
α-helix	67-69	3
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-93	9	9
β-strand	96-99	4	9
β-strand	103-108	6	9
α-helix	109	1
β-strand	117-122	6	10
β-strand	130-135	6	10
α-helix	142-144	3
β-strand	152-153	2	10
α-helix	154-156	3
β-strand	157-161	5	10
β-strand	166-174	9	10
α-helix	182-187	6

Chain E: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	11
β-strand	11-15	5	12
β-strand	20-22	3	13
β-strand	23-26	4	11
β-strand	32-38	7	12
β-strand	45-51	7	12
β-strand	54-58	5	12
β-strand	65-68	4	13
β-strand	74	1	11
β-strand	76-79	4	13
α-helix	84-86	3
β-strand	88-95	8	12
α-helix	103-104	2
β-strand	105-106	2	12
β-strand	110-115	6	12
β-strand	122	1	14
α-helix	123-124	2
β-strand	125-129	5	15
β-strand	130	1	10
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	15
β-strand	152	1	14
β-strand	156-162	7	16
β-strand	165-167	3	16
β-strand	171-173	3	15
β-strand	178-181	4	15
β-strand	184-194	11	15
α-helix	195-198	4
β-strand	204-211	8	16
β-strand	214	1	17
α-helix	225-226	2
β-strand	228	1	17
β-strand	230-237	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A	protein	281	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Heat shock factor protein 2	C	protein	9	Mus musculus	P38533 (AlphaFold model)
47BE7 TCR alpha chain	D	protein	191	Mus musculus
47BE7 TCR beta chain	E	protein	263	Mus musculus

Sequence of entity 1 (A), FASTA

>7NA5_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A)
MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEY
WERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYE
GRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATL
LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPST

Sequence of entity 2 (B), FASTA

>7NA5_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7NA5_3 Heat shock factor protein 2 (chains C)
YGFRNVVHI

Sequence of entity 4 (D), FASTA

>7NA5_4 47BE7 TCR alpha chain (chains D)
MQQKVQQSPESLIVPEGGMASLNCTFSDRNSQYFWWYRQHSGEGPKALMSIFSNGDKKEG
RFTAHLNKASLHVSLHIKDSQPSDSALYFCAVSNYNVLYFGSGTKLTVEPNIQNPEPAVY
QLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGAIAWSNQTS
FTCQDIFKETN

Sequence of entity 5 (E), FASTA

>7NA5_5 47BE7 TCR beta chain (chains E)
MDPKIIQKPKYLVAVTGSEKILICEQYLGHNAMYWYRQSAKKPLEFMFSYSYQKLMDNQT
ASSRFQPQSSKKNHLDLQITALKPDDSATYFCASSQEPGGYAEQFFGPGTRLTVLEDLRN
VTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKE
SNYSYSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRA
DCGITSASYQQGGSGGSHHHHHH

Primary citation

Structure of the TCR-H2DB ternary complex with melanoma HSF2 neoantigen YGFRNVVHI. Patskovsky, Y., Finnigan, J., Patskovska, L. et al. To be published.

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

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